ETNK1

ethanolamine kinase 1

Basic information

Region (hg38): 12:22625075-22690665

Links

ENSG00000139163 ∙ NCBI:55500 ∙ OMIM:609858 ∙ HGNC:24649 ∙ Uniprot:Q9HBU6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ETNK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ETNK1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	13	0	0

Variants in ETNK1

This is a list of pathogenic ClinVar variants found in the ETNK1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-22625167-C-G		not specified	Uncertain significance (Mar 16, 2022)
12-22625188-A-G		not specified	Uncertain significance (Jun 01, 2023)
12-22625233-T-G		not specified	Uncertain significance (Jun 17, 2024)
12-22625251-C-T		not specified	Uncertain significance (Sep 17, 2021)
12-22625270-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-22625455-C-G		not specified	Uncertain significance (Mar 31, 2024)
12-22625482-A-T		not specified	Uncertain significance (May 30, 2024)
12-22625500-C-G		not specified	Uncertain significance (Apr 18, 2023)
12-22625510-A-T		not specified	Uncertain significance (Jan 31, 2024)
12-22625523-G-C		not specified	Uncertain significance (Jan 24, 2024)
12-22625579-C-A		not specified	Uncertain significance (Nov 08, 2024)
12-22643850-A-C		not specified	Uncertain significance (May 06, 2024)
12-22643928-C-G		not specified	Uncertain significance (Mar 06, 2023)
12-22644219-C-T		Teratoma	Uncertain significance (Jan 01, 2023)
12-22661076-A-G		not specified	Uncertain significance (Oct 04, 2022)
12-22661079-C-G		not specified	Uncertain significance (Aug 01, 2024)
12-22661099-G-T		not specified	Uncertain significance (Jul 05, 2023)
12-22661198-G-C		not specified	Uncertain significance (Jul 05, 2024)
12-22673534-T-G		not specified	Uncertain significance (Jan 24, 2024)
12-22673611-C-T		not specified	Uncertain significance (Mar 25, 2024)
12-22673622-G-A		not specified	Uncertain significance (Mar 07, 2023)
12-22684901-A-G		not specified	Uncertain significance (Oct 07, 2024)
12-22684946-C-G		not specified	Uncertain significance (Dec 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ETNK1	protein_coding	protein_coding	ENST00000266517	8	65591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.926	0.0744	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	161	245	0.656	0.0000115	2930
Missense in Polyphen		30	88.175	0.34023		1123
Synonymous	-0.0325	95	94.6	1.00	0.00000438	875
Loss of Function	3.70	3	21.5	0.139	0.00000105	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000444	0.000428
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000551	0.0000462
European (Non-Finnish)	0.0000490	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Highly specific for ethanolamine phosphorylation. May be a rate-controlling step in phosphatidylethanolamine biosynthesis.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Kennedy pathway from Sphingolipids;One carbon metabolism and related pathways;Metabolism of lipids;Metabolism;Synthesis of PE;phosphatidylethanolamine biosynthesis II;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.292
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.164
• hipred: Y
• hipred_score: 0.648
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Etnk1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: phosphatidylethanolamine biosynthetic process;phosphorylation
• Cellular component: nucleoplasm;cytosol;plasma membrane;membrane
• Molecular function: ethanolamine kinase activity;protein binding;ATP binding